Generally the most common way to kill invading organisms involved in infection of a host is exposure to specific chemicals, which interfere in their metabolism without substantially deleteriously affecting the host. These chemicals could include antibiotics and antivirals and are in wide use.
However some organisms such as viruses live inside the cells and are not treatable with antibiotics. Further, some infections present in those tissues which have poor blood supply can result in a chronic deep-seated infection for example osteomyelitis. Further, if the host's immune system is compromised, such as in some cases of HIV then usually mild infections can spread rapidly. Still further, many bacteria have developed a resistance to the commonly used antibiotics.
In general, many different micro-organisms can invade a host, including the human body, and reside there. Some can cause only mild problems and eventually are destroyed by the host's immune system—others can cause recurring problems or kill the host. Various treatments have been devised to treat these organisms such as antiseptics, antibiotics or antivirals. Several factors can affect the efficacy of treatment such as:                Site of infection (poor blood supply)        Nature of organism i.e. does it exist outside cells where antibiotics can reach it or        Some organisms such as viruses reside within the host cells and cannot be reached        Development of resistance to antibiotics.        
Herpes viruses living inside the body cells are difficult to destroy without harming the host. When the virus is first transmitted in the case of genital herpes—usually via sexual contact—it causes a reaction in the skin consisting of painful blisters.
These eventually heal but the virus particles are not destroyed by the ‘immune system’. Instead they migrate to the bottom of the spine into clumps of nerve cells called the dorsal ganglia. The dormant virus particles can stay there indefinitely and at times of physical or emotional stress they travel back down the nerves to approximately the same area of skin to cause further blistering. This cycle can repeat indefinitely.